Shadowing fishermen's nets with a robot sub

On a cold, clear day in November, the Donna Kathleen rode a gelid swell off the central California coast. On the aft deck of the 58-foot vessel, a small knot of people in hard hats ministered to what looked like a glorified toboggan with a couple of thrusters bolted on.

The fridge-sized, black-and-seafoam-green machine, dubbed the Beagle, was a remotely operated vehicle, or ROV — essentially, a boxy, unmanned robot submarine. As a veteran ROV designer named Dirk Rosen fiddled with one of the video cameras mounted on it, he waxed decidedly un-lyrical about the machine’s inherent hydrodynamic flair.

“It’s a total brick," said Rosen. "It’s basically a pickup truck carrying a whole bunch of sensors.”

As Rosen paid out a thick umbilical cord attached to the Beagle, a crane lifted the machine over the deck railing and gently set it into the water, where it bobbed on the swell. Then the ROV burst to life. Like a dog sniffing out a scent, the Beagle zipped 20 feet through the water and then burbled into the dark depths below.

Rosen turned and ducked through a hatchway into the Box, a darkened, van-sized container lashed to the deck of the boat. Inside, James Lindholm, a professor from California State University Monterey Bay, sat crammed into a seat with what looked like a video-game controller in his hand. A miniature disco ball dangled over his left shoulder, and as his iPod shuffled through its play list, the groove of the Bee Gees’ “Night Fever” suddenly began bumping over the soft hum of electronics cooling fans.

Lindholm’s eyes were riveted on a bank of video monitors displaying a feed from the Beagle. Five hundred feet below, at the edge of the Continental Shelf, the ROV whirred along the path that a 240-foot-wide fishing net had left as it dragged along the sandy seafloor — an obvious furrow carved by the half-ton steel “doors” that had kept the net pressed to the bottom. As Lindholm “flew” the Beagle, Mary Gleason, a biologist from the Nature Conservancy perched on a seat next to him, clicking a joystick and taking one photo of the bottom after another.

Everything about the effort had been painstakingly choreographed, right down to the path of the drag net they were following. A week earlier, a trawler called the South Bay had intentionally towed its net through this experimental plot and three others, as part of a carefully constructed experiment to investigate the effects of trawling on the habitat of bottom-dwelling species such as soles and eel pouts.

Bottom trawling is notorious as the most destructive form of fishing; some fisheries scientists have likened trawling coral reefs to clear-cutting the rainforest. Yet while the impacts of trawlers on reefs has been exhaustively studied, scientists have only a sketchy understanding of what trawling does to other types of habitats, and how — or whether — those areas recover after they’ve been “dragged.”

“There’s just a handful of people doing trawl-related research worldwide,” says Lindholm, “and outside of really charismatic habitats, we don’t know very much.” Lindholm has eschewed Cousteauvian coral wonderlands to focus on “soft-sediment environments”: seemingly featureless, current-swept expanses that, he concedes, “are not exactly like what you see in National Geographic.”

Technically, soft-sediment environments are composed primarily of sand, although Lindholm tends to just call it mud. Whatever you call them, however, they are a very important chunk of the planet. They make up about 70 percent of the continental shelf off California and are the most abundant habitat on earth. “Even if we think mud’s not that exciting, said Lindholm, “we can’t ignore it.”

Still, the work is hardly the kind of thing that makes fifth-graders thrill with dreams of a degree in marine biology. “We’re down there just plowing through transects for eight hours straight,” Lindholm said. “That is a long time to be slowly moving over the mud.”

Up at the helm of the Donna Kathleen, Tim Maricich babied the throttles. His boat was a shrimper that has been repurposed as a research vessel, and Maricich conceded that he was still getting used to the new kind of work. “We’re working in friggin’ meters,” he groused. “My whole life has been feet and fathoms, and now everything’s in meters.”

Two years ago, The Nature Conservancy cut a deal to buy out the trawl permits for the struggling fleet of boats based in the Central Coast port town of Morro Bay. Working with the Pacific Fishery Management Council, the conservancy established 3.8 million acres of “essential fish habitat” — essentially a giant no-trawl zone.

A handful of Morro Bay boats are now back on the water, fishing not with trawl nets but more discriminating gear like longlines and traps.   But with the end of dragging in the area, Lindholm and Gleason also realized that they had a ready-made, real-world laboratory for a controlled study of trawling. They teamed up with Rosen — who, after a career as an ROV engineer, now runs a nonprofit called Marine Applied Research and Exploration — and bought the Beagle with funding from the California Ocean Protection Council.

Last November, the South Bay dragged the experimental plots for the first time, and the Donna Kathleen followed two weeks later with the ROV. Earlier this year, the researchers returned for a six-month checkup, and they’ll return once more this fall. Then they’ll drag the plots again, more intensively, and repeat the process for the next three years.

• Wildlife